This, all of this, is so complex, widespread, and deeply embedded that I don't know if even killing Johan could stop any of it. It's not that the whole world is evil – Tenma keeps coming across good people, too – it's just that this isn't something killing one person could solve. Tenma's efforts seem futile.

So, now we know that Johan and Nina

were intentionally bred as part of some kind of program. That last scene seems like an indicator that it was Nina who came home to find Johan dressed as her, which would fit with my theory that it was Nina at the mansion. I guess Johan was dressing as Nina even back when they were children.